[gmx-users] mpi run in Gromacs 4.5.3

[Mark Abraham]

On 14/12/2010 7:48 AM, Te, Jerez A., Ph.D. wrote:
>
> Hi,
> I have been trying to run Gromacs 4.5.3 parallel simulations using 
> openmpi 1.4.2. From my understanding, mdrun_mpi is not used in this 
> version of Gromacs.
>

I don't understand what (you think) you mean. You can use thread-based 
parallelism for processors that share common silicon, or MPI-based 
parallelism if a network connection is involved, but not both. The 
latter is named mdrun_mpi by default.

> Our system administrator told me that all mpi related options have 
> been turned on while installing Gromacs. With either commands:
> mdrun -np X -deffnm topol -N X (run in an 8-cpu node)
>

This won't run in parallel at all. mdrun ignores -np and -N

> or
> mpirun -np X mdrun -deffnm topol -N X (submitted in a number of nodes 
> depending on availability)
>

This will get you the symptoms below, but -N is still ignored.

> I get X identical simulations instead of a parallel run. If X=4, I get 
> 4 identical simulations (the same simulation ran 4 times) instead of 1 
> parallel simulation in 4 processors. The performance difference 
> between a single-processor run and the X=4 run are also similar (no 
> marked difference in the time it takes to finish the simulation).
> Has anyone encountered this problem?
>

You're using a serial mdrun. Use a parallel mdrun.

Mark
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